[gmx-users] NPT system density

[Erik Marklund]

Hi,

For one thing; to keep density constant (as in fixed) you want NVT, not 
NPT. NPT could, depending on your starting state, allow for initial 
drift in the system size.

Cheers,

Erik Marklund

Moeed skrev:
> Hello,
>
> I have 125 hexane molecules in a box of 0.25nm3. The desnity I 
> calculate from this number of molecules is approx. 71000 Kg/m3. To 
> make sure that the density remains constant I am doing NPT simulation. 
> From this simulation I see the density is 577 Kg/m3. and the volume is 
> 30 nm3. Please guide me why is this...also how can I get the 
> compressibility for my system?
>
>
>  *Volume                      30.9568   0.374111   0.204815  
> -0.108427   -1.08449
> Density (SI)                577.914    6.97804    3.80252    
> 2.02643    20.2684*
>
>
> Thanks,
>
>
>
> Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 21 data sets
> The term 'Cons. rmsd ()' is averaged over 501 frames
> All other averages are exact over 5001 steps
>
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Angle                       4390.56    265.163    204.663    
> 58.3917    584.034
> Ryckaert-Bell.              986.833    112.503    83.3767    
> 26.1601    261.653
> LJ-14                       649.581    30.9116    28.8685    
> 3.82766    38.2843
> Coulomb-14                 -289.755     25.871    9.19928     
> 8.3746    83.7628
> LJ (SR)                    -3367.85    62.5126    55.3718   -10.0486   
> -100.506
> Coulomb (SR)                675.839    21.1543    7.92426   -6.79315   
> -67.9451
> Coul. recip.                 927.32    22.6843    7.25885    -7.4434   
> -74.4489
> Potential                   3972.53    379.824    316.992     
> 72.469    724.835
> Kinetic En.                 6331.94    257.353     242.79    
> 29.5579    295.639
> Total Energy                10304.5    567.222    484.728    
> 102.027    1020.47
> Temperature                 297.366     12.086    11.4021    
> 1.38812     13.884
> Pressure (bar)             -30.0299    746.524    745.665   -12.3992   
> -124.017
> Cons. rmsd ()            3.73576e-06 2.80181e-07 2.35022e-07 
> 5.28277e-08 5.28383e-07
> Box-X                       4.98423  0.0200728  0.0109722 -0.00582152 
> -0.0582268
> Box-Y                       2.49212  0.0100364  0.0054861 -0.00291076 
> -0.0291134
> *Volume                      30.9568   0.374111   0.204815  
> -0.108427   -1.08449
> Density (SI)                577.914    6.97804    3.80252    
> 2.02643    20.2684*
> pV                         -55.9879    1393.39    1391.81   -22.9985   
> -230.031
> #Surf*SurfTen                218.21    4871.45    4871.37   -9.30662   
> -93.0848
> T-HEX                       297.366     12.086    11.4021    
> 1.38812     13.884
> Lamb-HEX                    1.00011 0.000588089 0.000561362 
> -6.07045e-05 -0.000607166
> Heat Capacity Cv:      12.5027 J/mol K (factor = 0.0016519)
> Isothermal Compressibility: 0.00011012 /bar
> Adiabatic bulk modulus:        9080.99  bar
>
> mdp file:
>
> title               = Hexane
> cpp                 = /lib/cpp
>
> ;        Run control
> integrator          =  md
> dt                  =  0.002        ; ps !
> nsteps              =  5000        ; total 1.0 ps.
> nstcomm             =  1        ; frequency for center of mass motion 
> removal   
>
> ;        Output control
> nstenergy           =  10        ; frequency to write energies to 
> energy file. i.e., energies and other statistical data are stored 
> every 10 steps
> nstxout             =  10        ; frequency to write 
> coordinates/velocity/force to output trajectory file
> nstvout             =  0
> nstfout             =  10
> nstlog              =  10        ; frequency to write energies to log file
> nstxtcout          =  10   
>
> ;        Neighbor searching
> nstlist             =  10        ; neighborlist will be updated at 
> least every 10 steps 
> ;ns_type             =  grid
>
> ;        Electrostatics/VdW
> coulombtype         =  PME         
> vdw-type            =  cut-off
> ;        Cut-offs
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
>
> ;        Temperature coupling    Berendsen temperature coupling is on 
> in two groups
> Tcoupl              =  berendsen
> tc-grps             =  HEX      ;sol
> tau_t               =  0.1      ;0.1
> ref_t               =  300      ;300
>
> ;        Pressure coupling:     Pressure coupling is not on
> Pcoupl              =  berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
>
> ;        Velocity generation    Generate velocites is on at 300 K. 
> Manual p155
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
> ;        Bonds
> constraints         =  all-bonds
> constraint-algorithm = lincs
>
> pbc=xyz
>
>
>
>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/